<i>HDACs</i> Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in <i>Prunus mume</i>
Histone deacetylases (HDACs) play important roles in plant growth, development, and stress response. However, the pattern of how they are expressed in response to cold stress in the ornamental woody plant <i>Prunus mume</i> is poorly understood. Here, we identify 121 <i>RoHDACs<...
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MDPI AG
2022-05-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/11/5957 |
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| author | Juan Meng Zhenying Wen Mingyu Li Tangren Cheng Qixiang Zhang Lidan Sun |
| author_facet | Juan Meng Zhenying Wen Mingyu Li Tangren Cheng Qixiang Zhang Lidan Sun |
| author_sort | Juan Meng |
| collection | DOAJ |
| description | Histone deacetylases (HDACs) play important roles in plant growth, development, and stress response. However, the pattern of how they are expressed in response to cold stress in the ornamental woody plant <i>Prunus mume</i> is poorly understood. Here, we identify 121 <i>RoHDACs</i> from eight Rosaceae plants of which 13 <i>PmHDACs</i> genes are from <i>P. mume</i>. A phylogenetic analysis suggests that the <i>RoHDACs</i> family is classified into three subfamilies, <i>HDA1/RPD3</i>, <i>HD2,</i> and <i>SIR2</i>. We identify 11 segmental duplication gene pairs of <i>RoHDACs</i> and find, via a sequence alignment, that the <i>HDACs</i> gene family, especially the plant-specific <i>HD2</i> family, has experienced gene expansion and contraction at a recent genome evolution history. Each of the three <i>HDACs</i> subfamilies has its own conserved domains. The expression of <i>PmHDACs</i> in mei is found to be tissue-specific or tissue-wide. RNA-seq data and qRT-PCR experiments in cold treatments suggest that almost all <i>PmHDACs</i> genes—especially <i>PmHDA1/6/14</i>, <i>PmHDT1</i>, and <i>PmSRT1/2</i>—significantly respond to cold stress. Our analysis provides a fundamental insight into the phylogenetic relationship of the <i>HDACs</i> family in Rosaceae plants. Expression profiles of <i>PmHDACs</i> in response to cold stress could provide an important clue to improve the cold hardiness of mei. |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T01:17:15Z |
| publishDate | 2022-05-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-8f0d1bb3206f4d1e8c74ac18311000572023-11-23T14:07:03ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-05-012311595710.3390/ijms23115957<i>HDACs</i> Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in <i>Prunus mume</i>Juan Meng0Zhenying Wen1Mingyu Li2Tangren Cheng3Qixiang Zhang4Lidan Sun5Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, ChinaBeijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, ChinaBeijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, ChinaBeijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, ChinaBeijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, ChinaBeijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, ChinaHistone deacetylases (HDACs) play important roles in plant growth, development, and stress response. However, the pattern of how they are expressed in response to cold stress in the ornamental woody plant <i>Prunus mume</i> is poorly understood. Here, we identify 121 <i>RoHDACs</i> from eight Rosaceae plants of which 13 <i>PmHDACs</i> genes are from <i>P. mume</i>. A phylogenetic analysis suggests that the <i>RoHDACs</i> family is classified into three subfamilies, <i>HDA1/RPD3</i>, <i>HD2,</i> and <i>SIR2</i>. We identify 11 segmental duplication gene pairs of <i>RoHDACs</i> and find, via a sequence alignment, that the <i>HDACs</i> gene family, especially the plant-specific <i>HD2</i> family, has experienced gene expansion and contraction at a recent genome evolution history. Each of the three <i>HDACs</i> subfamilies has its own conserved domains. The expression of <i>PmHDACs</i> in mei is found to be tissue-specific or tissue-wide. RNA-seq data and qRT-PCR experiments in cold treatments suggest that almost all <i>PmHDACs</i> genes—especially <i>PmHDA1/6/14</i>, <i>PmHDT1</i>, and <i>PmSRT1/2</i>—significantly respond to cold stress. Our analysis provides a fundamental insight into the phylogenetic relationship of the <i>HDACs</i> family in Rosaceae plants. Expression profiles of <i>PmHDACs</i> in response to cold stress could provide an important clue to improve the cold hardiness of mei.https://www.mdpi.com/1422-0067/23/11/5957histone deacetylase <i>HDACs</i> familyphylogenetic analysis<i>Prunus mume</i>cold stress |
| spellingShingle | Juan Meng Zhenying Wen Mingyu Li Tangren Cheng Qixiang Zhang Lidan Sun <i>HDACs</i> Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in <i>Prunus mume</i> International Journal of Molecular Sciences histone deacetylase <i>HDACs</i> family phylogenetic analysis <i>Prunus mume</i> cold stress |
| title | <i>HDACs</i> Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in <i>Prunus mume</i> |
| title_full | <i>HDACs</i> Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in <i>Prunus mume</i> |
| title_fullStr | <i>HDACs</i> Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in <i>Prunus mume</i> |
| title_full_unstemmed | <i>HDACs</i> Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in <i>Prunus mume</i> |
| title_short | <i>HDACs</i> Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in <i>Prunus mume</i> |
| title_sort | i hdacs i gene family analysis of eight rosaceae genomes reveals the genomic marker of cold stress in i prunus mume i |
| topic | histone deacetylase <i>HDACs</i> family phylogenetic analysis <i>Prunus mume</i> cold stress |
| url | https://www.mdpi.com/1422-0067/23/11/5957 |
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